Make sure you read this
http://www.revisionfx.com/generalfaqsMVMaya.htm
Most Common Mistakes: Not setting Custom Alpha on (so no alpha in MV pass). Assume one can use alpha of color pass in MV but then render color pass with MB off and MV pass with shutter set to 0.5 0.5 which puts both results half a frame apart
Without more specifics it's hard to help
Feel free to send to techsupport@revisionfx.com one MV frame and 2 color frames (the color counterpart and the frame after or before so we have a rough idea of the actual action)
Pierre
